All of them indicate large differences 70%-89% between Human and Chimpanzee, which is in contrast to generally accepted difference between 94%-98%.
Psst ... you mean similarities, not differences.
Now, is it "in contrast to" the generally accepted figure? Well, if it was, their results would have been meaningful, and they could have published them in a real journal. But what they've actually done is picked a different method of measuring difference. Your weight in kilograms is not
in contrast to your weight in ounces, it's just a different metric.
I think these numbers are taken by different method than previous high similarity results.
Yes.
Now the ideal metric for difference would be one that measures the number of mutations needed to get from one genome to the other; this would be biologically meaningful. As Taq points out, the creationists are ignoring the possibility of indels, so they get a different and less meaningful figure. But it's larger, which is what they're aiming for. But by doing that, they've rendered worthless their conclusion that "this defies standard evolutionary time-scales".
4) Further research: By the same method compare DNA between species inside one baramin (e.g. mouse and rat).
An excellent idea.
From the data I can find, humans and chimps should be further apart than the two sequenced species of macaques, which belong to the same genus; maybe a little further apart than a domestic cat and a tiger; and closer than a rat and a mouse. If the latter is the case, the creationists would be hoist on their own petard.
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The paper speaks approvingly of
this guy. The web page makes his perl scripts freely available, so it should be easy enough to re-use his techniques on other genomes.